for users who dont like to code or type, a simple GUI for lossless packaging of RAW audio data (or RAW video data) is
yamb. i even prefer that to fixing FLV's with FLV Fix tools.
For example, when you (losslessly) extract *.264 and *.aac with FLVExtract and you then try to package them as *.mp4 with yamb, then use the "Avg Frame Rate" (and not the "True Frame Rate") displayed by FLVExtract. yamb sometimes ask you to enter "frame rate", sometimes it doesnt.
If the MP4 is still out of sync (audio vs. video), then use as "frame rate" the "videoframerate" as seen by "FLV Fix" (Replay Media Catcher 4) after you have fixed the FLV with "Fix Duration".